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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ), 'gf_id' => 'HOM05D001284', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001284' ), 'data_identifier' => 'HOM05D001284', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001284', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03570' => 'bna', 'A03p33120' => 'bna', 'A04p25370' => 'bna', 'A05p12670' => 'bna', 'A05p44320' => 'bna', 'A08p00580' => 'bna', 'A09p26550' => 'bna', 'A10p03500' => 'bna', 'A10p22720' => 'bna', 'Aa31LG11G13180' => 'aar', 'Aa31LG1G19320' => 'aar', 'Aa31LG1G19760' => 'aar', 'Aa31LG5G13270' => 'aar', 'Aa31LG5G4620' => 'aar', 'Aa31LG9G9950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1095' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.374' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1352' => 'aag', 'Actinidia09750' => 'ach', 'Actinidia10796' => 'ach', 'Actinidia13732' => 'ach', 'Ah.02g120130' => 'amhyb', 'Ah.04g158970' => 'amhyb', 'Ah.06g195500' => 'amhyb', 'Ah.09g234410' => 'amhyb', 'AL1G14740' => 'aly', 'AL3G12210' => 'aly', 'AL4G28480' => 'aly', 'AL6G27420' => 'aly', 'AL6G47740' => 'aly', 'Aqoxy125s003' => 'aox', 'Aqoxy1G02899' => 'aox', 'Aqoxy1G04176' => 'aox', 'Aqoxy2G02674' => 'aox', 'Aqoxy2G04071' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2W3ULI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37HJXT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7H2PG3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8X5LLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9YBE2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CC7STI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FY8RTQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J4T639' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SW9R8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHA4F3' => 'arhy', 'AT1G05000' => 'ath', 'AT2G32960' => 'ath', 'AT3G02800' => 'ath', 'AT4G03960' => 'ath', 'AT5G16480' => 'ath', 'ATR0171G019' => 'atr', 'ATR1128G008' => 'atr', 'ATR1136G052' => 'atr', 'Atru.chr10.2313' => 'acertr', 'Atru.chr12.1789' => 'acertr', 'Atru.chr6.3262' => 'acertr', 'AUR62000313' => 'cqu', 'AUR62006658' => 'cqu', 'AUR62012767' => 'cqu', 'AUR62015124' => 'cqu', 'AUR62017584' => 'cqu', 'BcaB01g01778' => 'bca', 'BcaB02g10510' => 'bca', 'BcaB04g19387' => 'bca', 'BcaB04g21401' => 'bca', 'BcaB06g28644' => 'bca', 'BcaB08g36848' => 'bca', 'BcaC02g07872' => 'bca', 'BcaC02g11362' => 'bca', 'BcaC03g18494' => 'bca', 'BcaC04g18874' => 'bca', 'BcaC04g21265' => 'bca', 'BcaC05g30506' => 'bca', 'BcaNung04310' => 'bca', 'BcaNung06791' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00280' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00300' => 'bna', 'BolC1t05870H' => 'bol', 'BolC2t06756H' => 'bol', 'BolC3t16295H' => 'bol', 'BolC4t23208H' => 'bol', 'BolC4t27725H' => 'bol', 'BolC5t29099H' => 'bol', 'BolC5t35065H' => 'bol', 'BolC9t56201H' => 'bol', 'BolC9t58900H' => 'bol', 'BraA01t04614Z' => 'bra', 'BraA02t05328Z' => 'bra', 'BraA03t12482Z' => 'bra', 'BraA04t18040Z' => 'bra', 'BraA05t20205Z' => 'bra', 'BraA06t23288Z' => 'bra', 'BraA09t38229Z' => 'bra', 'BraA10t42626Z' => 'bra', 'BraA10t44332Z' => 'bra', 'BraA10t44335Z' => 'bra', 'C02p08380' => 'bna', 'C03p40300' => 'bna', 'C04p16560' => 'bna', 'C04p62480' => 'bna', 'C05p03190' => 'bna', 'C09p27400' => 'bna', 'C09p33680' => 'bna', 'C09p60690' => 'bna', 'C09p75920' => 'bna', 'CAN.G1186.8' => 'can', 'CAN.G463.5' => 'can', 'CAN.G503.12' => 'can', 'CAN.G694.26' => 'can', 'CAN.G784.2' => 'can', 'CANSAT54G0248' => 'cansat', 'CANSAT56G1823' => 'cansat', 'CANSAT64G1303' => 'cansat', 'CARHR004420' => 'chi', 'CARHR076810' => 'chi', 'CARHR104140' => 'chi', 'CARHR126900' => 'chi', 'CARHR196750' => 'chi', 'CARHR253440' => 'chi', 'Carub.0001s0425' => 'cru', 'Carub.0003s0190' => 'cru', 'Carub.0004s1439' => 'cru', 'Carub.0006s1468' => 'cru', 'Carub.0006s3203' => 'cru', 'Ca_06058_v3' => 'car', 'Ca_07981_v3' => 'car', 'Ca_21055_v3' => 'car', 'CBR_g23883' => 'cbr', 'CBR_g23885' => 'cbr', 'CBR_g29374' => 'cbr', 'CBR_g30804' => 'cbr', 'Cc05_g02830' => 'ccan', 'Cc09_g01090' => 'ccan', 'Cc09_g03610' => 'ccan', 'CDE05G0832' => 'cde', 'CDE05G3210' => 'cde', 'CDE07G1364' => 'cde', 'Cfa006266' => 'cfa', 'Cfa014313' => 'cfa', 'Ciclev10012810m.g' => 'ccl', 'Ciclev10016646m.g' => 'ccl', 'Ciclev10016786m.g' => 'ccl', 'CiPaw.03G154700' => 'cil', 'CiPaw.04G109600' => 'cil', 'CiPaw.07G079900' => 'cil', 'CiPaw.08G115200' => 'cil', 'CiPaw.09G099900' => 'cil', 'CiPaw.10G075700' => 'cil', 'ClCG02G018090' => 'cla', 'ClCG03G010730' => 'cla', 'ClCG09G011180' => 'cla', 'COL.COLO4_19816' => 'col', 'COL.COLO4_21891' => 'col', 'COL.COLO4_31849' => 'col', 'Cpa.g.sc132.28' => 'cpa', 'Cpa.g.sc152.60' => 'cpa', 'Cpa.g.sc1741.1' => 'cpa', 'CsaV3_1G044550' => 'csa', 'CsaV3_6G015410' => 'csa', 'CsaV3_6G037790' => 'csa', 'CSS0005678' => 'camsi', 'CSS0006266' => 'camsi', 'CSS0009170' => 'camsi', 'CSS0009364' => 'camsi', 'CSS0024728' => 'camsi', 'CSS0031682' => 'camsi', 'CSS0046214' => 'camsi', 'DCAR_019256' => 'dca', 'DCAR_019740' => 'dca', 'DCAR_020971' => 'dca', 'DCAR_021138' => 'dca', 'Dinv08714' => 'din', 'Dinv09890' => 'din', 'Dinv09891' => 'din', 'Dinv29106' => 'din', 'Dinv39753' => 'din', 'Duzib106G1471' => 'dzi', 'Duzib128G1540' => 'dzi', 'Duzib133G1472' => 'dzi', 'Duzib138G1065' => 'dzi', 'Duzib177G0655' => 'dzi', 'Duzib211G0128' => 'dzi', 'Duzib235G0405' => 'dzi', 'ECA232G4831' => 'eca', 'ECA236G4476' => 'eca', 'ECA238G2959' => 'eca', 'ECA238G4178' => 'eca', 'ECA240G2703' => 'eca', 'EL10Ac4g09971' => 'bvu', 'EL10Ac6g13268' => 'bvu', 'EL10Ac7g15875' => 'bvu', 'EL10Ac8g20145' => 'bvu', 'EL10Ac9g22828' => 'bvu', 'Eucgr.A01094' => 'egr', 'Eucgr.B01414' => 'egr', 'Eucgr.E03975' => 'egr', 'FAN02G2581' => 'fan', 'FAN02G4375' => 'fan', 'FAN05G0279' => 'fan', 'FAN05G0794' => 'fan', 'FAN05G2789' => 'fan', 'FAN09G1823' => 'fan', 'FAN09G2270' => 'fan', 'FAN12G0233' => 'fan', 'FAN14G4280' => 'fan', 'FAN14G4691' => 'fan', 'FvH4_4g32730' => 'fve', 'FvH4_6g00520' => 'fve', 'FvH4_6g42080' => 'fve', 'Glyma.02G267900' => 'gma', 'Glyma.07G264400' => 'gma', 'Glyma.09G250700' => 'gma', 'Glyma.10G170900' => 'gma', 'Glyma.14G049600' => 'gma', 'Glyma.18G241800' => 'gma', 'Glyma.20G221250' => 'gma', 'Gohir.A05G391500' => 'ghi', 'Gohir.A06G152200' => 'ghi', 'Gohir.A07G084200' => 'ghi', 'Gohir.A07G168600' => 'ghi', 'Gohir.A07G187600' => 'ghi', 'Gohir.A10G010600' => 'ghi', 'Gohir.A13G154300' => 'ghi', 'Gohir.D04G025800' => 'ghi', 'Gohir.D06G158500' => 'ghi', 'Gohir.D07G090300' => 'ghi', 'Gohir.D07G175100' => 'ghi', 'Gohir.D07G194400' => 'ghi', 'Gohir.D10G010300' => 'ghi', 'Gohir.D13G159000' => 'ghi', 'Gorai.001G096500' => 'gra', 'Gorai.001G195900' => 'gra', 'Gorai.001G217500' => 'gra', 'Gorai.010G185200' => 'gra', 'Gorai.011G011300' => 'gra', 'Gorai.012G028400' => 'gra', 'Gorai.013G179700' => 'gra', 'GSVIVG01007270001' => 'vvi', 'GSVIVG01019113001' => 'vvi', 'GSVIVG01030509001' => 'vvi', 'HanXRQChr02g0039681' => 'han', 'HanXRQChr04g0126871' => 'han', 'HanXRQChr15g0468611' => 'han', 'HanXRQChr16g0506401' => 'han', 'Haze_04551' => 'cav', 'Haze_06888' => 'cav', 'Haze_12762' => 'cav', 'Hma1.2p1_0000F.1_g000550' => 'hma', 'Hma1.2p1_0003F.1_g003740' => 'hma', 'Hma1.2p1_0171F.1_g075530' => 'hma', 'Hma1.2p1_0177F.1_g078100' => 'hma', 'Hma1.2p1_0298F.1_g117370' => 'hma', 'Hma1.2p1_0445F.1_g154280' => 'hma', 'HPP92_001408' => 'vpl', 'HPP92_004742' => 'vpl', 'HPP92_010860' => 'vpl', 'HPP92_010885' => 'vpl', 'HPP92_010892' => 'vpl', 'HPP92_017329' => 'vpl', 'Hund07345' => 'sun', 'Hund21899' => 'sun', 'Hund23418' => 'sun', 'Hund24226' => 'sun', 'Lalb_Chr02g0149451' => 'lal', 'Lalb_Chr03g0038481' => 'lal', 'Lalb_Chr04g0250011' => 'lal', 'Lalb_Chr07g0177061' => 'lal', 'Lalb_Chr10g0105561' => 'lal', 'Lalb_Chr17g0347251' => 'lal', 'Lalb_Chr21g0311451' => 'lal', 'Lj1C782G8' => 'lonja', 'Lj1g0024005' => 'lja', 'Lj2C263G3' => 'lonja', 'Lj4g0024144' => 'lja', 'LjContig00029g0027058' => 'lja', 'Lju4319C0G4' => 'lonja', 'Lsat_1_v5_gn_2_18221' => 'lsa', 'Lsat_1_v5_gn_7_14401' => 'lsa', 'Lsat_1_v5_gn_7_95141' => 'lsa', 'Lsat_1_v5_gn_9_106001' => 'lsa', 'Lsat_1_v5_gn_9_48960' => 'lsa', 'Manes.12G006000' => 'mes', 'Manes.12G069200' => 'mes', 'Manes.13G005700' => 'mes', 'Manes.13G065700' => 'mes', 'Mapoly0037s0101' => 'mpo', 'Mapoly0049s0032' => 'mpo', 'Mapoly0137s0032' => 'mpo', 'Mapoly0152s0034' => 'mpo', 'MBI07_g06135_MAGBIO' => 'mbi', 'MD04G1244500' => 'mdo', 'MD05G1354200' => 'mdo', 'MD09G1115000' => 'mdo', 'MD09G1115100' => 'mdo', 'MD10G1328400' => 'mdo', 'MD12G1260400' => 'mdo', 'MD16G1025100' => 'mdo', 'MD17G1106400' => 'mdo', 'MD17G1221400' => 'mdo', 'MD17G1221500' => 'mdo', 'Medtr4g132810' => 'mtr', 'Medtr5g085300' => 'mtr', 'Medtr7g079970' => 'mtr', 'MELO3C010061.2' => 'cme', 'MELO3C014438.2' => 'cme', 'MELO3C019734.2' => 'cme', 'Migut.M00421' => 'egut', 'Migut.M01362' => 'egut', 'MSTRG.14862' => 'ama', 'MSTRG.7188' => 'ama', 'Nitab4.5_0000083g0180' => 'nta', 'Nitab4.5_0000130g0150' => 'nta', 'Nitab4.5_0000143g0510' => 'nta', 'Nitab4.5_0000751g0040' => 'nta', 'Nitab4.5_0000971g0110' => 'nta', 'Nitab4.5_0001198g0310' => 'nta', 'Nitab4.5_0001308g0040' => 'nta', 'Nitab4.5_0001537g0010' => 'nta', 'Nitab4.5_0006830g0010' => 'nta', 'Nitab4.5_0012850g0020' => 'nta', 'Nn1g03370' => 'nnu', 'Nn1g07308' => 'nnu', 'Nn1g09758' => 'nnu', 'Oeu007122.1' => 'oeu', 'Oeu049718.1' => 'oeu', 'Oeu061770.1' => 'oeu', 'Os02g0771400' => 'osa', 'Os06g0208700' => 'osa', 'Os09g0135700' => 'osa', 'Os12g0420300' => 'osa', 'Peaxi162Scf00063g00310' => 'pax', 'Peaxi162Scf00156g00112' => 'pax', 'Peaxi162Scf00253g00723' => 'pax', 'Peaxi162Scf00344g01012' => 'pax', 'Peaxi162Scf01333g00139' => 'pax', 'PGR031G0029' => 'pgr', 'PGR042G2743' => 'pgr', 'PGR119G2421' => 'pgr', 'PGSC0003DMG400006429' => 'stu', 'PGSC0003DMG400007258' => 'stu', 'PGSC0003DMG400023475' => 'stu', 'PGSC0003DMG400027222' => 'stu', 'PGSC0003DMG402013333' => 'stu', 'Phvul.003G082500' => 'pvu', 'Phvul.007G118300' => 'pvu', 'Phvul.008G054300' => 'pvu', 'Phvul.008G214300' => 'pvu', 'Potri.002G224000' => 'ptr', 'Potri.004G002800' => 'ptr', 'Potri.011G021100' => 'ptr', 'Potri.013G086500' => 'ptr', 'Potri.014G159100' => 'ptr', 'Pp3c12_21270' => 'ppa', 'Pp3c1_32070' => 'ppa', 'Pp3c20_2620' => 'ppa', 'Pp3c20_2950' => 'ppa', 'Pp3c23_18160' => 'ppa', 'Pp3c24_18350' => 'ppa', 'Pp3c24_520' => 'ppa', 'Pp3c2_3020' => 'ppa', 'Prupe.1G328300' => 'ppe', 'Prupe.3G209500' => 'ppe', 'Prupe.4G013600' => 'ppe', 'Prupe.5G070300' => 'ppe', 'Prupe.6G361100' => 'ppe', 'Psat0s715g0040' => 'psa', 'Psat2g025520' => 'psa', 'Psat2g111880' => 'psa', 'Psat3g058840' => 'psa', 'Psat3g138320' => 'psa', 'Psat4g003680' => 'psa', 'Psat5g072640' => 'psa', 'Psat5g114120' => 'psa', 'Psat7g180240' => 'psa', 'Psat7g216800' => 'psa', 'Psat7g250840' => 'psa', 'PSO017G4234' => 'pso', 'PSO070G0001' => 'pso', 'PSO070G0002' => 'pso', 'PSO210G5119' => 'pso', 'PSO339G3351' => 'pso', 'PSO339G4507' => 'pso', 'PSO384G4492' => 'pso', 'PSO403G0002' => 'pso', 'PSO541G3946' => 'pso', 'PSO675G1644' => 'pso', 'PSO675G3255' => 'pso', 'PSO675G7702' => 'pso', 'PSO832G3418' => 'pso', 'QL01p048423' => 'qlo', 'QL03p008144' => 'qlo', 'QL05p070137' => 'qlo', 'QL08p030474' => 'qlo', 'RcHm_v2.0_Chr2g0158001' => 'rch', 'RcHm_v2.0_Chr3g0447901' => 'rch', 'RcHm_v2.0_Chr4g0441711' => 'rch', 'Rhsim04G0049700' => 'rsi', 'Rhsim06G0167600' => 'rsi', 'Rhsim09G0130000' => 'rsi', 'Sabra02G0171500' => 'sbr', 'Sabra04G0001300' => 'sbr', 'Sabra11G0011300' => 'sbr', 'Sabra11G0013100' => 'sbr', 'Sabra13G0077600' => 'sbr', 'Sabra14G0120900' => 'sbr', 'SalBow7G3360' => 'sbo', 'SalBow8G4042' => 'sbo', 'Sc05g0009490' => 'sci', 'Sc06g0005060' => 'sci', 'Sc06g0009690' => 'sci', 'Sc09g0001490' => 'sci', 'Sc12g0002060' => 'sci', 'Sc16g0010370' => 'sci', 'Sed0001746' => 'sed', 'Sed0009769' => 'sed', 'Sed0018332' => 'sed', 'Sed0018856' => 'sed', 'Sed0027892' => 'sed', 'Sed0028165' => 'sed', 'SEGI_09437' => 'sgi', 'SEGI_15601' => 'sgi', 'SEGI_17448' => 'sgi', 'SEGI_21520' => 'sgi', 'SEGI_22894' => 'sgi', 'SEGI_25252' => 'sgi', 'SGA_v2.0_scaffold34G13790' => 'sas', 'SGA_v2.0_scaffold7G03791' => 'sas', 'SMO115G0332' => 'smo', 'SMO119G0421' => 'smo', 'SMO137G0265' => 'smo', 'SMO203G0214' => 'smo', 'SMO259G0035' => 'smo', 'Solyc04g056340.4' => 'sly', 'Solyc05g052770.1' => 'sly', 'Solyc05g055740.4' => 'sly', 'Solyc07g049560.3' => 'sly', 'Solyc11g011970.2' => 'sly', 'Sopen04g025240' => 'spe', 'Sopen05g034150' => 'spe', 'Sopen07g024920' => 'spe', 'Sopen11g006780' => 'spe', 'Sp1g03880' => 'spa', 'Sp3g01830' => 'spa', 'Sp4g15320' => 'spa', 'Sp6g04750' => 'spa', 'Sp6g27680' => 'spa', 'TAR020G0006' => 'tar', 'TAR365G0231' => 'tar', 'TAR624G0054' => 'tar', 'TAR626G1409' => 'tar', 'TAR629G2136' => 'tar', 'THA.LOC104801010' => 'tha', 'THA.LOC104813361' => 'tha', 'THA.LOC104813479' => 'tha', 'THA.LOC104816034' => 'tha', 'THA.LOC104820916' => 'tha', 'THA.LOC104827175' => 'tha', 'Thecc.01G182800' => 'tca', 'Thecc.05G199400' => 'tca', 'Thecc.06G229900' => 'tca', 'Thhalv10008768m.g' => 'esa', 'Thhalv10014713m.g' => 'esa', 'Thhalv10017110m.g' => 'esa', 'Thhalv10021545m.g' => 'esa', 'Thhalv10028976m.g' => 'esa', 'TPR.G25659' => 'tpr', 'TPR.G30353' => 'tpr', 'TPR.G37050' => 'tpr', 'TWI18G1256' => 'twi', 'TWI18G1409' => 'twi', 'TWI36G1189' => 'twi', 'TWI38G1064' => 'twi', 'TWI75G0057' => 'twi', 'unitig_0.g728' => 'ugi', 'unitig_37.g12159' => 'ugi', 'unitig_92.g28112' => 'ugi', 'vmacro09367' => 'vma', 'vmacro10406' => 'vma', 'vmacro12159' => 'vma', 'VMungo0647G2165' => 'vmu', 'VMungo0720G1054' => 'vmu', 'VMungo1215G0107' => 'vmu', 'VMungo1383G2017' => 'vmu', 'Zm00001eb095500' => 'zma', 'Zm00001eb193370' => 'zma', 'Zm00001eb256300' => 'zma', 'Zm00001eb278930' => 'zma', 'Zm00001eb373490' => 'zma' ) $gf_id = 'HOM05D001284' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001284' ) $data_identifier = 'HOM05D001284' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 6, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 8, 'ppe' => (int) 5, 'psa' => (int) 11, 'pso' => (int) 13, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 2, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373490' $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